From 113497c42f4881fe77fd7e1ab1697500766ceeb8 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 3 Mar 2026 17:04:50 +0000 Subject: [PATCH 1/4] Testing R5 Backport Testing R5 Backport --- package.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package.json b/package.json index d81fd4e0..ce113ee0 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,8 @@ "hl7.fhir.uv.ips": "1.1.0", "hl7.fhir.eu.laboratory": "0.1.0-ballot", "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", - "ihe.iti.pcf": "1.0.0-comment" + "ihe.iti.pcf": "1.0.0-comment", + "hl7.fhir.uv.xver-r5.r4.r4": "0.0.1-snapshot-2" }, "fhirVersions": [ "4.0.1" From c43fdff97841fec06e2ec1574b5f999f49b7376a Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 5 Mar 2026 09:01:32 +0000 Subject: [PATCH 2/4] Testing with UKCOre 0.28.0 Testing with UKCOre 0.28.0 --- fhirpkg.lock.json | 2 +- package.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 024fdfd8..061ab16a 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,7 @@ "hl7.fhir.uv.ips": "1.1.0", "fhir.dicom": "2022.4.20221006", "hl7.fhir.eu.laboratory": "0.1.0-ballot", - "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "ihe.iti.pcf": "1.0.0-comment", "us.nlm.vsac": "0.9.0", "ihe.iti.balp": "1.1.1", diff --git a/package.json b/package.json index ce113ee0..ec81a033 100644 --- a/package.json +++ b/package.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", "hl7.fhir.uv.ips": "1.1.0", "hl7.fhir.eu.laboratory": "0.1.0-ballot", - "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "ihe.iti.pcf": "1.0.0-comment", "hl7.fhir.uv.xver-r5.r4.r4": "0.0.1-snapshot-2" }, From 513b35fc538691ea76e66f98e6448c035d365890 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 5 Mar 2026 10:11:53 +0000 Subject: [PATCH 3/4] Update DiagnosticReport-GenomicVariantAssessment-Example. Update DiagnosticReport-GenomicVariantAssessment-Example. --- ...port-GenomicVariantAssessment-Example.json | 333 +++++++++--------- fhirpkg.lock.json | 4 +- package.json | 2 +- 3 files changed, 170 insertions(+), 169 deletions(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index 0c7ca4b7..0bd9a307 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -1,183 +1,182 @@ { - "resourceType": "DiagnosticReport", - "id": "DiagnosticReport-GenomicVariantAssessment-Example", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", - "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" - ] + "resourceType": "DiagnosticReport", + "id": "DiagnosticReport-GenomicVariantAssessment-Example", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", + "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition", + "valueReference": { + "reference": "Composition/Composition-EULabGenomicReport-Example" + } }, - "extension": [ - { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition", - "valueReference": { - "reference": "Composition/Composition-EULabGenomicReport-Example" - } - }, - { - "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", - "valueReference": { - "reference": "Task/Task-FollowupRecommendationReport-Example", - "display": "Confirmatory testing recommended" - } - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", - "valueRelatedArtifact": { - "type": "citation", - "display": "Johnson et al 2012 (PMID22740598)" - } - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", - "valueRelatedArtifact": { - "type": "citation", - "display": "Foley et al 2014 (PMID22740598)" - } - }, - { - "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note", - "valueAnnotation": { - "extension": [ - { - "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code", - "valueCodeableConcept": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs", - "code": "test-disclaimer" - } - ] - } - } - ], - "text": "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." - } - } - ], - "basedOn": [ - { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" - } - ], - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" - } - ] - }, - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1236877003", - "display": "Genetic pathology" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51969-4", - "display": "Genetic analysis report" - }, - { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report" - } - ] + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", + "valueReference": { + "reference": "Task/Task-FollowupRecommendationReport-Example", + "display": "Confirmatory testing recommended" + } }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" + { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", + "valueRelatedArtifact": { + "type": "citation", + "display": "Johnson et al 2012 (PMID22740598)" + } }, - "effectiveDateTime": "2023-10-16T00:00:00-05:00", - "issued": "2023-09-16T00:00:00-05:00", - "performer": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "specimen": [ - { - "reference": "Specimen/Specimen-PheobeSmitham-Example" - } - ], - "media": [ - { - "link": { - "type":"DocumentReference", - "display": "Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition.", - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", - "valueCode": "unsupported" - } - ] - }, - "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", + "valueRelatedArtifact": { + "type": "citation", + "display": "Foley et al 2014 (PMID22740598)" + } + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note", + "valueAnnotation": { + "extension": [ + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code", + "valueCodeableConcept": { + "coding": [ { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", - "valueReference": { - "reference": "DocumentReference/DocumentReference-StructureReporting-Example" - } + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs", + "code": "test-disclaimer" } - ] + ] + } + } + ], + "text": "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." + } + } + ], + "basedOn": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE" } - ], - "result": [ - { - "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example", - "display": "Brown-Vialetto-Van Laere syndrome type 2" - }, + ] + }, + { + "coding": [ { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" } - ], - "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).", - "conclusionCode": [ + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51969-4", + "display": "Genetic analysis report" + }, + { + "system": "http://snomed.info/sct", + "code": "1054161000000101", + "display": "Genetic report" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "effectiveDateTime": "2023-10-16T00:00:00-05:00", + "issued": "2023-09-16T00:00:00-05:00", + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "specimen": [ + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + } + ], + "media": [ + { + "link": { + "type": "DocumentReference", + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "extension": [ { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6576-8", - "display": "Positive" - }, - { - "system": "http://snomed.info/sct", - "code": "10828004", - "display": "Positive" - } - ] + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", + "valueReference": { + "reference": "DocumentReference/DocumentReference-StructureReporting-Example" + } + } + ] + } + ], + "result": [ + { + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example", + "display": "Brown-Vialetto-Van Laere syndrome type 2" + }, + { + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + } + ], + "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).", + "conclusionCode": [ + { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6576-8", + "display": "Positive" }, { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "699866005", - "display": "Brown-Vialetto-Van Laere syndrome" - } - ] + "system": "http://snomed.info/sct", + "code": "10828004", + "display": "Positive" } - ], - "presentedForm": [ + ] + }, + { + "coding": [ { - "contentType": "application/pdf", - "language": "en-GB", - "url": "https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1", - "size": 43272, - "title": "Genomic Report for Pheobe Smitham", - "creation": "2023-10-16" + "system": "http://snomed.info/sct", + "code": "699866005", + "display": "Brown-Vialetto-Van Laere syndrome" } - ] + ] + } + ], + "presentedForm": [ + { + "contentType": "application/pdf", + "language": "en-GB", + "url": "https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1", + "size": 43272, + "title": "Genomic Report for Pheobe Smitham", + "creation": "2023-10-16" + } + ] } \ No newline at end of file diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 061ab16a..0515a1bf 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,5 +1,5 @@ { - "updated": "2025-12-17T17:33:35.7803726+00:00", + "updated": "2026-03-05T09:19:44.2705434+00:00", "dependencies": { "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", @@ -8,8 +8,10 @@ "hl7.fhir.eu.laboratory": "0.1.0-ballot", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "ihe.iti.pcf": "1.0.0-comment", + "hl7.fhir.r4b.core": "4.3.0", "us.nlm.vsac": "0.9.0", "ihe.iti.balp": "1.1.1", + "hl7.fhir.uv.xver-r5.r4": "0.0.1-snapshot-2", "hl7.terminology.r4": "6.5.0", "hl7.fhir.uv.extensions.r4": "5.2.0" }, diff --git a/package.json b/package.json index ec81a033..32631a4e 100644 --- a/package.json +++ b/package.json @@ -9,7 +9,7 @@ "hl7.fhir.eu.laboratory": "0.1.0-ballot", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "ihe.iti.pcf": "1.0.0-comment", - "hl7.fhir.uv.xver-r5.r4.r4": "0.0.1-snapshot-2" + "hl7.fhir.uv.xver-r5.r4": "0.0.1-snapshot-2" }, "fhirVersions": [ "4.0.1" From 719ba5befa9fa8e7dbafd462c4d3f31aa2abad00 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 5 Mar 2026 10:26:16 +0000 Subject: [PATCH 4/4] Update DiagnosticReport-GenomicVariantAssessment-Example Update DiagnosticReport-GenomicVariantAssessment-Example --- ...Report-GenomicVariantAssessment-Example.json | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index 0bd9a307..e4a4bdba 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -116,22 +116,19 @@ "media": [ { "link": { - "type": "DocumentReference", "extension": [ + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", + "valueReference": { + "reference": "DocumentReference/DocumentReference-StructureReporting-Example" + } + }, { "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", "valueCode": "unsupported" } ] - }, - "extension": [ - { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", - "valueReference": { - "reference": "DocumentReference/DocumentReference-StructureReporting-Example" - } - } - ] + } } ], "result": [